Once you’ve done a system transfer, your 3DS is automatically “wiped”, and set up again as if it were new. Using my guide you actually take your card out of your old 3DS and put it in your new one, so there’s no old card still in your old 3DS. However, if you did have an old card (e.g. you transferred from an old SD to a new microSD before doing the system transfer) then once you’ve confirmed everything works on your New 3DS and new microSD card, you can wipe the old card yourself. It’s files won’t work in you old 3DS any more. They probably won’t cause problems, but they won’t be accessible so you may as well wipe it.